# A tibble: 618 × 20
Genome Genome_type Length N_contigs N50 GC_content Completeness
<chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
1 MGYG000303700 MAG 678213 2 466332 47.8 63.7
2 MGYG000303701 MAG 1500176 18 112881 42.4 87.8
3 MGYG000303702 MAG 1210062 44 48790 26.4 94.8
4 MGYG000303703 MAG 1706016 27 89653 44.6 93.7
5 MGYG000303704 MAG 703182 7 111709 47.8 63.7
6 MGYG000303705 MAG 2542045 112 34925 48 97.9
7 MGYG000303706 MAG 1449687 185 10153 34.8 85.2
8 MGYG000303707 MAG 1874692 90 28768 37.1 99.0
9 MGYG000303708 MAG 1480380 12 169949 42.2 87.6
10 MGYG000303709 MAG 694644 57 15063 47.9 62.0
# ℹ 608 more rows
# ℹ 13 more variables: Contamination <dbl>, rRNA_5S <dbl>, rRNA_16S <dbl>,
# rRNA_23S <dbl>, tRNAs <dbl>, Genome_accession <chr>, Species_rep <chr>,
# Lineage <chr>, Sample_accession <chr>, Study_accession <chr>,
# Country <chr>, Continent <chr>, FTP_download <chr>Exploring meta-data of human vaginal microbiome
Group 6
DATA DESCRIPTION
- 618 vaginal metagenome-assembled genomes (MAGs)
- 25 variables covering taxonomy, assembly quality, and geography
- High completeness and low contamination for most genomes
- Dataset dominated by a few major bacterial phyla
- Genome lengths fall within biologically expected ranges
Most MAGs belong to only a few dominant phyla.
This indicates strong taxonomic skew in the dataset.
Genome lengths fall within the expected biological range
for vaginal bacterial taxa (typically 1.5–3 Mb).
The majority of the data this study are from USA and China. This creates an uneven geographic distribution, which limits how confidently we can compare countries.
ANALYSIS 1 - Phylogenetic tree
- Constructed a phylogenetic tree from the taxonomic ranks (Domain → Species) in the augmented dataset.
- NA values in taxonomy were removed before tree construction.
- The tree is colored by phylum to show taxonomic clustering.
ANALYSIS 2 - Data quality
Investigating the quality of samples.
- Scatterplot of completeness (%) vs. contamination (%) for all MAGs
- The dashed lines mark the high-quality genomes (above 90% completeness and below 5% contamination)
- Points are colored by phylum
- Most MAGs cluster in the high-quality area indicating good assemble quality of the MAGs.
ANALYSIS 3 - Associated and non-associated-endometriosis MAGs
- Compared endometriosis-associated vs non-associated MAGs
- Focused on GC content, genome length, completeness & contamination
- Investigated whether associated MAGs cluster taxonomically
- Goal: determine if associated MAGs form a genomically distinct group
Endometriosis-associated MAGs occur in only a few phyla.
Most phyla contain no associated MAGs, suggesting limited taxonomic clustering.
GC content ranges overlap almost completely.
No evidence that GC% distinguishes associated vs non-associated MAGs.
ANALYSIS 4 - Taxa Distribution between countries
- Investigating the distribution of taxa in Countries
- Filtered for NA in Countries
- Counted taxa instances for each country and converted to wide format
- Big difference in sample size –> normalized data
Some variation between countries. I.e. Order Bacteroidales, but not much.
Could’ve tested for significance.
Only two principal components –> 100% variance.
Clear division of countries.
Along PC1, Fusobacteria and Bacteroidota (order = Bacteroidales). Correlation with heatmap.
Test to see if there is a significant difference in the proportion of endometriosis-associated genomes between countries
| country1 | country2 | p_value | odds_ratio | CI_low | CI_high |
|---|---|---|---|---|---|
| USA | China | 0.0205 | 2.670 | 1.113 | 7.779 |
| USA | Denmark | 0.1554 | 4.648 | 0.738 | 193.498 |
| Denmark | China | 1.0000 | 0.576 | 0.012 | 5.077 |
- Significant difference between USA and China
- USA displayed 2.7 times higher odds of endometriosis-associated genomes
- No significant difference between USA vs. Denmark or Denmark vs. China
- Likely due to the limited amount of danish and chinese genomes represented